Sonja Nowotschin, PhD

Senior Research Scientist

Pictured: Sonja Nowotschin

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Education & Training


Research Associate, Developmental Biology Program, Sloan Kettering Institute (lab of Kat Hadjantonakis)


Postdoctoral Fellow, Developmental Biology Program, Sloan Kettering Institute (lab of Kat Hadjantonakis)


Postdoctoral Fellow, Albert Einstein College of Medicine (lab of Bernice Morrow)


Graduate studies, University of Karlsruhe, Germany and Albert Einstein College of Medicine, New York (lab of Dr Bernice Morrow)

Thesis title: “Genetic interaction of Tbx1 and Pitx2 is required for early heart development”


Undergraduate studies in English, Spanish, French and Italian at the Faculty of Translation Studies, Linguistics and Cultural Studies, Johannes Gutenberg University of Mainz


Research Student, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Germany (lab of Martin Blum)


MSc degree, University of Karlsruhe, Germany (lab of Dr Martin Blum)

Thesis title: “Expression of the homeobox gene Pitx2 during mouse embryogenesis”


Undergraduate studies in biology, University of Karlsruhe, Germany

Research Interests

My research interests center on investigating tissue morphogenesis and patterning in the mouse embryo around the time of gastrulation with the aim of providing a blueprint for understanding analogous events in human embryonic development. My work focuses on elucidating the role of T-box transcription factors and their co-factors and targets in regulating cell states and cell behavior.

In humans, mutations in T-box genes are responsible for developmental dysmorphic syndromes, and several T-box factors have been implicated in the genesis and progression of cancer.

As a graduate student my work focused on the role of Tbx1, a gene implicated in the etiology of DiGeorge syndrome in humans, in cardiovascular development and function in a mouse model. My ongoing studies focus on the roles Eomesodermin (Eomes) and Tbx6, two T-box factors that are critical for the specification of two distinct cell lineages: the embryonic visceral endoderm in the pre-gastrula stage embryo, and the presomitic mesoderm at gastrulation.

I recently demonstrated that Eomes is essential for anterior-posterior axis specification and for anterior visceral endoderm (AVE) recruitment, while Tbx6 is necessary for the specification of the presomitic mesoderm, the tissue progenitor of the vertebral column, and the axial skeletal muscles.

An open question concerns how T-box factors operate at a molecular level to direct cell behavior and cell fate. To gain further insight into the functions of Eomes and Tbx6, I am elucidating the gene regulatory networks in which these factors operate, as well as their interactomes.


Nowotschin S, Costello I, Piliszek A, Kwon GS, Mao CA, Klein WH, Robertson EJ, Hadjantonakis AK. The T-box transcription factor Eomesodermin is essential for AVE induction in the mouse embryo. Genes Dev. 2013 27(9):997-1002.

Nowotschin S, Xenopoulos P, Schrode N, Hadjantonakis AK. A bright single-cell resolution live imaging reporter of Notch signaling in the mouse. BMC Dev Biol. 2013 13:15.

Nowotschin S, Ferrer-Vaquer A, Concepcion D, Papaioannou VE, Hadjantonakis AK.

Interaction of Wnt3a, Msgn1 and Tbx6 in neural versus paraxial mesoderm lineage commitment and paraxial mesoderm differentiation in the mouse embryo. Dev Biol. 2012 367(1):1-14.

Xenopoulos P, Nowotschin S, Hadjantonakis AK. Live imaging fluorescent proteins in early mouse embryos. Methods Enzymol. 2012;506:361-89.

Viotti M, Nowotschin S, Hadjantonakis AK. Afp::mCherry, a red fluorescent transgenic reporter of the mouse visceral endoderm. Genesis. 2011 49(3):124-33.

Isern J, He Z, Fraser ST, Nowotschin S, Ferrer-Vaquer A, Moore R, Hadjantonakis AK, Schulz V, Tuck D, Gallagher PG, Baron MH. Single-lineage transcriptome analysis reveals key regulatory pathways in primitive erythroid progenitors in the mouse embryo. Blood. 2011 117(18):4924-34.

Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z. A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. BMC Bioinformatics. 2010 11:580.

Nowotschin S, Ferrer-Vaquer A, Hadjantonakis AK. Imaging mouse development with confocal time-lapse microscopy. Methods Enzymol. 2010; 476:351-77.

Nowotschin S, Hadjantonakis AK. Cellular dynamics in the early mouse embryo: from axis formation to gastrulation. Curr Opin Genet Dev. 2010 20(4):420-7.

Nowotschin S, Hadjantonakis AK. Photomodulatable fluorescent proteins for imaging cell dynamics and cell fate. Organogenesis. 2009 5(4):135-44.

Nowotschin S, Hadjantonakis AK.Use of KikGR a photoconvertible green-to-red fluorescent protein for cell labeling and lineage analysis in ES cells and mouse embryos.

BMC Dev Biol. 2009 9:49.

Nowotschin S, Eakin GS, Hadjantonakis AK. Dual transgene strategy for live visualization of chromatin and plasma membrane dynamics in murine embryonic stem cells and embryonic tissues. Genesis. 2009 47(5):330-6.

Nowotschin S, Eakin GS, Hadjantonakis AK. Live-imaging fluorescent proteins in mouse embryos: multi-dimensional, multi-spectral perspectives. Trends Biotechnol. 2009 27(5):266-76.

Liao J, Aggarwal VS, Nowotschin S, Bondarev A, Lipner S, Morrow BE. Identification of downstream genetic pathways of Tbx1 in the second heart field.

Dev Biol. 2008 Apr 15;316(2):524-37.

Nowotschin S, Liao J, Gage PJ, Epstein JA, Campione M, Morrow BE. Tbx1 affects asymmetric cardiac morphogenesis by regulating Pitx2 in the secondary heart field. Development. 2006 133(8):1565-73.

Arnold JS, Werling U, Braunstein EM, Liao J, Nowotschin S, Edelmann W, Hebert JM, Morrow BE. Inactivation of Tbx1 in the pharyngeal endoderm results in 22q11DS malformations. Development. 2006 133(5):977-87.

Liao J, Kochilas L, Nowotschin S, Arnold JS, Aggarwal VS, Epstein JA, Brown MC, Adams J, Morrow BE. Full spectrum of malformations in velo-cardio-facial syndrome/DiGeorge syndrome mouse models by altering Tbx1 dosage. Hum Mol Genet. 2004 13(15):1577-85.

Raft S, Nowotschin S, Liao J, Morrow BE. Suppression of neural fate and control of inner ear morphogenesis by Tbx1. Development. 2004 131(8):1801-12.

Campione M, Steinbeisser H, Schweickert A, Deissler K, van Bebber F, Lowe LA, Nowotschin S, Viebahn C, Haffter P, Kuehn MR, Blum M. The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. Development. 1999 126(6):1225-34.